Kyoto Encyclopedia Of Genes And Genomes Pathway Analysis Research Articles

Identification of core cuprotosis-correlated biomarkers in abdominal aortic aneurysm immune microenvironment based on bioinformatics.

The occurrence of abdominal aortic aneurysms (AAAs) is related to the disorder of immune microenvironment. Cuprotosis was reported to influence the immune microenvironment. The objective of this study is to identify cuprotosis-related genes involved in the pathogenesis and progression of AAA. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) in mouse were identified following AAA through high-throughput RNA sequencing. The enrichment analyses of pathway were selected through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG). The validation of cuprotosis-related genes was conducted through immunofluorescence and western blot analyses. Totally, 27616 lncRNAs and 2189 mRNAs were observed to be differentially expressed (|Fold Change| ≥ 2 and q< 0.05) after AAA, including 10424 up-regulated and 17192 down-regulated lncRNAs, 1904 up-regulated and 285 down-regulated mRNAs. Gene ontology and KEGG pathway analysis showed that the DElncRNAs and DEmRNAs were implicated in many different biological processes and pathways. Furthermore, Cuprotosis-related genes (NLRP3, FDX1) were upregulated in the AAA samples compared with the normal one. Cuprotosis-related genes (NLRP3,FDX1) involved in AAA immune environment might be critical for providing new insight into identification of potential targets for AAA therapy.

Identification of Differentially Expressed Genes and Molecular Pathways Involved in Osteoclastogenesis Using RNA-seq.

Osteoporosis is a disease that is characterised by reduced bone mineral density (BMD) and can be exacerbated by the excessive bone resorption of osteoclasts (OCs). Bioinformatic methods, including functional enrichment and network analysis, can provide information about the underlying molecular mechanisms that participate in the progression of osteoporosis. In this study, we harvested human OC-like cells differentiated in culture and their precursor peripheral blood mononuclear cells (PBMCs) and characterised the transcriptome of the two cell types using RNA-sequencing in order to identify differentially expressed genes. Differential gene expression analysis was performed in RStudio using the edgeR package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to identify enriched GO terms and signalling pathways, with inter-connected regions characterised using protein-protein interaction analysis. In this study, we identified 3201 differentially expressed genes using a 5% false discovery rate; 1834 genes were upregulated, whereas 1367 genes were downregulated. We confirmed a significant upregulation of several well-established OC genes including CTSK, DCSTAMP, ACP5, MMP9, ITGB3, and ATP6V0D2. The GO analysis suggested that upregulated genes are involved in cell division, cell migration, and cell adhesion, while the KEGG pathway analysis highlighted oxidative phosphorylation, glycolysis and gluconeogenesis, lysosome, and focal adhesion pathways. This study provides new information about changes in gene expression and highlights key biological pathways involved in osteoclastogenesis.

MicroRNAs-mediated regulation of the differentiation of dental pulp-derived mesenchymal stem cells: a systematic review and bioinformatic analysis

BackgroundHuman dental pulp-derived mesenchymal stem cells (hDP-MSCs), which include human dental pulp stem cells (hDPSCs) and stem cells from human exfoliated deciduous teeth (SHEDs), are promising cell sources for regenerative therapies. Nevertheless, a lack of knowledge relating to the mechanisms regulating their differentiation has limited their clinical application. microRNAs (miRNAs) are important regulatory molecules in cellular processes including cell differentiation. This systematic review aims to provide a panel of miRNAs that regulate the differentiation of hDP-MSCs including hDPSCs and SHEDs. Additionally, bioinformatic analyses were conducted to discover target genes, signaling pathways and gene ontologies associated with the identified miRNAs.MethodsA literature search was performed in MEDLINE (via PubMed), Web of Science, Scopus, Embase and Cochrane Library. Experimental studies assessing the promotive/suppressive effect of miRNAs on the differentiation of hDP-MSCs and studies evaluating changes to the expression of miRNAs during the differentiation of hDP-MSCs were included. miRNAs involved in odontogenic/osteogenic differentiation were then included in a bioinformatic analysis. A miRNA-mRNA network was constructed, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. A protein–protein interaction (PPI) network was also constructed.ResultsOf 766 initially identified records through database searching, 42 and 36 studies were included in qualitative synthesis and bioinformatic analyses, respectively. Thirteen miRNAs promoted and 17 suppressed odontogenic/osteogenic differentiation of hDP-MSCs. hsa-miR-140-5p, hsa-miR-218 and hsa-miR-143 were more frequently reported suppressing the odontogenic/osteogenic differentiation of hDP-MSCs. hsa-miR-221 and hsa-miR-124 promoted and hsa-miR-140-5p inhibited neuronal differentiation, hsa-miR-26a-5p promoted and hsa-miR-424 suppressed angiogenic differentiation, and hsa-miR-135 and hsa-miR-143 inhibited differentiation within myogenic lineages. A miRNA-mRNA network including 1890 nodes and 2171 edges was constructed. KEGG pathway analysis revealed MAPK, PI3K-Akt and FoxO as key signaling pathways involved in the odontogenic/osteogenic differentiation of hDP-MSCs.ConclusionsThe findings of this systematic review support the potential application of the specific miRNAs to regulate the directed differentiation of hDP-MSCs in the field of regenerative therapies.

Changes in gene expression and neuroinflammation in the hippocampus of rats with poststroke cognitive impairment.

Poststroke cognitive impairment (PSCI) often occurs during the stroke recovery period and greatly increases the difficulty of rehabilitation. Activation of neuroinflammation and long-term changes in gene expression patterns in the hippocampus could be essential in the development of PSCI. Therefore, this study aimed to identify neuroinflammation and changes in gene expression patterns in the hippocampus in rats with PSCI. Rats underwent transient middle cerebral artery occlusion (tMCAO) or sham surgery. The infarct volume was measured on day 3 after surgery. The Morris water maze (MWM) test was used to assess cognitive function. Microglial activation and white matter (WM) lesions in the hippocampus were evaluated on day 28 after surgery. In addition, we compared differentially expressed genes (DEGs) in the hippocampus between tMCAO group rats and sham group rats by RNA sequencing. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) network analyses were conducted to investigate these DEGs. The results showed that the tMCAO group rats showed extensive infarction and cognitive dysfunction compared with the sham group rats. Microglial activation and WM damage were obvious in the hippocampus of tMCAO group rats. We found 43 DEGs by RNA sequencing: 29 genes with upregulated expression and 14 genes with downregulated expression. The GO analysis indicated that DEGs were mainly involved in cell proliferation and differentiation, cholesterol synthesis, and metabolism. The KEGG pathway analysis suggested that the DEGs were significantly enriched in intestinal immune network for IgA production and steroid biosynthesis. Acta2, Calb2, and Cxcl12 were notable in the PPI analysis. Our results suggest that microglial activation and WM damage are maintained in rats with PSCI. The mechanism may be related to the regulation of steroid biosynthesis, intestinal immunity, and potential key genes such as Acta2, Calb2, and Cxcl12 in the hippocampus.

A Network Pharmacology Approach for Uncovering the Mechanism of 'Kouchuangling' in Radiation-induced Oral Mucositis Treatment.

Radiation-induced oral mucositis (RIOM) is an intractable inflammatory disease whose pathogenesis needs to be clarified. "Kouchuangling" (KCL), a traditional Chinese medicine formula, is composed of Lonicerae Japonicae Flos, Radix Paeoniae Rubra, and Radix Sanguisorbae. Although all of them are Chinese folk medicines which have long been utilized for ameliorating inflammation, the mechanism of KCL to RIOM remains unclear. To predict the active ingredients of KCL and identify the mechanism of KCL on RIOM. We identified the chemical ingredients in KCL using TCM Systems Pharmacology (TCMSP), TCM@Taiwan, PubChem, and SuperPred databases and used the oral bioavailability (OB), drug-like properties (DL) and Degree of compounds for screening. Targets for oral mucositis were obtained from the Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), PharmGKB, and DrugBank databases. Cytoscape 3.7.0 was used to visualize the compound-target-disease network for KCL and RIOM. The biological processes of target gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed using DAVID. Based on OB≥30%, DL≥0.18 and Degree≥3, 24 active ingredients and 960 targets on which the active components acted were identified. A total of 1387 targets for oral mucositis were screened. GO enrichment and KEGG pathway analyses resulted in 43 biological processes (BPs), 3 cell components (CCs), 5 molecular functions (MFs), and 32 KEGG pathways, including leishmaniasis, Toll-like receptor signaling, TNF signaling, and Influenza A pathways. This experiment preliminarily verified that the active ingredients of KCL play a role in the treatment of RIOM through multiple targets and pathways, providing a reference for further study of the pharmacological mechanism of Chinese herbal medicine.

Transcriptome Sequencing Reveals Autophagy Networks in Rat Livers during the Development of NAFLD and Identifies Autophagy Hub Genes

(1) Autophagy is an important biological process in cells and is closely associated with the development and progression of non-alcoholic fatty liver disease (NAFLD). Therefore, this study aims to investigate the biological function of the autophagy hub genes, which could be used as a potential therapeutic target and diagnostic markers for NAFLD. (2) Male C57BL/6J mice were sacrificed after 16 and 38 weeks of a high-fat diet, serum biochemical indexes were detected, and liver lobules were collected for pathological observation and transcriptome sequencing. The R software was used to identify differentially expressed autophagy genes (DEGs) from the transcriptome sequencing data of mice fed with a normal diet for 38 weeks (ND38) and a high-fat diet for 38 weeks (HFD38). Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on the DEGs, a protein-protein interaction (PPI) network of the DEGs was established using the STRING data website, and the results were visualized through Cytoscape. (3) After 16 weeks and 38 weeks of a high-fat diet, there was a significant increase in body weight, serum total cholesterol (TC), low-density lipoprotein-cholesterol (LDL-C) and triglycerides (TG) in mice, along with lipid accumulation in the liver, which was more severe at 38 weeks than at 16 weeks. The transcriptome data showed significant changes in the expression profile of autophagy genes in the livers of NAFLD mice following a long-term high-fat diet. Among the 31 differentially expressed autophagy-related genes, 13 were upregulated and 18 were downregulated. GO and KEGG pathway analysis revealed that these DEGs were primarily involved in autophagy, cholesterol transport, triglyceride metabolism, apoptosis, the FoxO signaling pathway, the p53 signaling pathway and the IL-17 signaling pathway. Four hub genes were identified by the PPI network analysis, of which Irs2, Pnpla2 and Plin2 were significantly downregulated, while Srebf2 was significantly upregulated by the 38-week high-fat diet. (4) The hub genes Irs2, Pnpla2, Srebf2 and Plin2 may serve as key therapeutic targets and early diagnostic markers in the progression of NAFLD.

Molecular targets of metformin against ovarian cancer based on network pharmacology.

The objective of this study was to analyze potential targets of metformin against ovarian cancer (OC) through network pharmacology. Pharmacodynamic targets of metformin were predicted using the Bioinformatics Analysis Tool for the molecular mechanism of traditional Chinese medicine (BATMAN), Drugbank, PharmMapper, SwissTargetPrediction, and TargetNet databases. R was utilized to analyze the gene expression of OC tissues, normal/adjacent noncancerous tissues, and screen differentially expressed genes (DEGs) in the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) + Genotype-Tissue Expression (GTEx) datasets. STRING 11.0 was utilized to explore the protein-protein interaction (PPI) of metformin target genes differentially expressed in OC. Cytoscape 3.8.0 was used to construct the network and screen the core targets. Additionally, gene ontology (GO) annotation and enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the common targets of metformin and OC through the DAVID 6.8 database. A total of 95 potential common targets of metformin and OC were identified from the intersection of 255 potential pharmacodynamic targets of metformin and 10,463 genes associated with OC. Furthermore, 10 core targets were screened from the PPI network [e.g., interleukin (IL) 1B, KCNC1, ESR1, HTR2C, MAOB, GRIN2A, F2, GRIA2, APOE, PTPRC]. In addition, it was shown in GO enrichment analysis that the common targets were mainly associated with biological processes (i.e., response to stimuli or chemical, cellular processes, and transmembrane transport), cellular components (i.e., plasma membrane, cell junction, and cell projection), and molecular functions (i.e., binding, channel activities, transmembrane transporter activity, and signaling receptor activities). Furthermore, it was indicated by KEGG pathway analysis that the common targets were enriched in metabolic pathways. The critical molecular targets and molecular pathways of metformin against OC were preliminarily determined by bioinformatics-based network pharmacology analysis, providing a basis, and reference for further experimental studies.

A high‐salt diet induces synaptic loss and memory impairment via gut microbiota and butyrate in mice

A high‐salt diet induces synaptic loss and memory impairment via gut microbiota and butyrate in mice

The Chromatin Remodeling Factor BrCHR39 Targets DNA Methylation to Positively Regulate Apical Dominance in Brassica rapa

The SHPRH (SNF2, histone linker, PHD, RING, helicase) subfamily belonging to ATP-dependent chromatin remodeling factor is the effective tumor-suppressor, which can polyubiquitinate PCNA (proliferating cell nuclear antigen) and participate in post-replication repair in human. However, little is known about the functions of SHPRH proteins in plants. In this study, we identified a novel SHPRH member BrCHR39 and obtained BrCHR39-silenced transgenic Brassica rapa. In contrast to wild-type plants, transgenic Brassica plants exhibited a released apical dominance phenotype with semi-dwarfism and multiple lateral branches. Furthermore, a global alteration of DNA methylation in the main stem and bud appeared after silencing of BrCHR39. Based on the GO (gene ontology) functional annotation and KEGG (Kyoto encyclopedia of genes and genomes) pathway analysis, the plant hormone signal transduction pathway was clearly enriched. In particular, we found a significant increase in the methylation level of auxin-related genes in the stem, whereas auxin- and cytokinin-related genes were hypomethylated in the bud of transgenic plants. In addition, further qRT-PCR (quantitative real-time PCR) analysis revealed that DNA methylation level always had an opposite trend with gene expression level. Considered together, our findings indicated that suppression of BrCHR39 expression triggered the methylation divergence of hormone-related genes and subsequently affected transcription levels to regulate the apical dominance in Brassica rapa.

Identification of the cuproptosis-related hub genes and therapeutic agents for sarcopenia.

Background: Along with acceleration of population aging, the increasing prevalence of sarcopenia has posed a heavy burden on families as well as society. In this context, it is of great significance to diagnose and intervene sarcopenia as early as possible. Recent evidence has indicated the role of cuproptosis in the development of sarcopenia. In this study, we aimed to seek the key cuproptosis-related genes that can be used for identification and intervention of sarcopenia. Methods: The GSE111016 dataset was retrieved from GEO. The 31 cuproptosis-related genes (CRGs) were obtained from previous published studies. The differentially expressed genes (DEGs) and Weighed gene co-expression network analysis (WGCNA) were subsequently analyzed. The core hub genes were acquired by the intersection of DEGs, WGCNA and CRGs. Through logistic regression analysis, we established a diagnostic model of sarcopenia based on the selected biomarkers and was validated in muscle samples from GSE111006 and GSE167186. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis were performed on these genes. Furthermore, the gene set enrichment analysis (GSEA), and immune cell infiltration were also conducted on the identified core genes. Finally, we screened the potential drugs targeting the potential biomarkers of sarcopenia. Results: A total of 902 DEGs and WGCNA containing 1,281 significant genes were preliminarily selected. Intersection of DEGs, WGCNA and CRGs yielded four core genes (PDHA1, DLAT, PDHB, and NDUFC1) as potential biomarkers for the prediction of sarcopenia. The predictive model was established and validated with high AUC values. KEGG pathway and Gene Ontology biological analysis indicated these core genes may play a crucial role in energy metabolism in mitochondria, oxidation process, and aging-related degenerative diseases. In addition, the immune cells may be involved in the development of sarcopenia through mitochondrial metabolism. Finally, metformin was identified as a promising strategy of sarcopenia treatment via targeting NDUFC1. Conclusion: The four cuproptosis-related genes PDHA1, DLAT, PDHB and NDUFC1 may be the diagnostic biomarkers for sarcopenia, and metformin holds great potential to be developed as a therapy for sarcopenia. These outcomes provide new insights for better understanding of sarcopenia and innovative therapeutic approaches.

Artesunate inhibits airway remodeling in asthma via the MAPK signaling pathway.

Background: Artesunate (ART), is a semi-synthetic water-soluble artemisinin derivative extracted from the plant Artemisia annua, which is often used to treating malaria. In vivo and in vitro studies suggested it may help decrease inflammation and attenuate airway remodeling in asthma. However, its underlying mechanism of action is not elucidated yet. Herein, an attempt is made to investigate the ART molecular mechanism in treating asthma. Methods: The BALB/c female mice sensitized via ovalbumin (OVA) have been utilized to establish the asthma model, followed by carrying out ART interventions. Lung inflammation scores by Haematoxylin and Eosin (H&E), goblet cell hyperplasia grade by Periodic Acid-Schiff (PAS), and collagen fibers deposition by Masson trichrome staining have been utilized for evaluating how ART affected asthma. RNA-sequencing (RNA-seq) analyses were performed to identify differentially expressed genes (DEGs). The DEGs were analyzed by Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and Protein-Protein interaction (PPI) function analyses. Hub clusters were found by Cytoscape MCODE. Subsequently, Real-Time quantitative PCR (RT-qPCR) verified the mRNA expression profiles of DEGs. Finally, immunohistochemistry (IHC) and western blots have validated the relevant genes and potential pathways. Results: ART considerably attenuated inflammatory cell infiltration, mucus secretion, and collagen fibers deposition. KEGG pathway analysis revealed that the ART played a protective role via various pathways including the mitogen-activated protein kinase (MAPK) pathway as one of them. Moreover, ART could alleviate the overexpression of found in inflammatory zone 1(FIZZ1) as revealed by IHC and Western blot analyses. ART attenuated OVA-induced asthma by downregulating phosphorylated p38 MAPK. Conclusion: ART exerted a protective function in a multitarget and multi-pathway on asthma. FIZZ1 was a possible target for asthma airway remodeling. The MARK pathway was one of the key pathways by which ART protected against asthma.

The NF-κB pathway plays a vital role in rat salivary gland atrophy model

ObjectiveThe aim of this study was to explore the histopathological and genetic changes in the submandibular glands after duct ligation and provide important clues to functional regeneration. DesignWe established a rat salivary gland duct ligation model and observed pathological changes in the rat submandibular gland on day 1 and weeks 1, 2, 3, and 4 using hematoxylin and eosin staining, Alcian blue–periodic acid Schiff staining, Masson staining, terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL), and immunohistochemical staining. RNA sequencing was performed on normal salivary glands and those from the ligation model after 1 week. Significantly differentially expressed genes were selected, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. ResultsApoptosis levels and histological and functional KEGG pathway analyses showed that injury to the salivary gland after ligation gradually increased. The TGF-β pathway was activated and promoted fibrosis. RNA sequencing results and further verification of samples at week 1 showed that the NF-κB pathway plays a vital role in salivary gland atrophy. ConclusionsOur results detailed the pathological changes in the submandibular gland after ligation and the important functions of the NF-κB pathway.

Abstract P2-03-20: Clinical profiling and comprehensive analysis of candidate genes related to breast cancer estrogen receptor intratumour heterogeneity

Abstract 1. Background and Aim Breast cancer has the highest incidence among the world’s population. One third of patients diagnosed with early breast cancer progressed into metastatic outcomes due to the inherent heterogeneity and evolutionary features of tumors. The main clinical manifestation is the discordance of receptor expression in metastases. ESR1 the estrogen receptor (ER) encoding gene, has been proved affected ER expression. Nevertheless, the correlation between ER transformation and the somatic mutation profiles in breast cancer metastatic lesions remains unclear. Availability of advanced high-throughput technologies, and the development of bioinformatics tools has greatly accelerated our cognition of the molecular basis of cancer. In this study, we aimed to evaluate the frequency, clinical characteristics and prognostic value of ER receptor conversion between primary and first metastatic lesions in 115 patients whose primary ER status are positive. We also compared the results of NGS of 42 patients and explored latent genes related to ER discordance in expression. 2. Method Qualified metastatic tumor tissue sequencing information was available for 42 patients. Samples were accessed using the FoundationOne CDx assay (Foundation Medicine, Cambridge, MA, USA) panel including 733 tumor related genes. High frequency mutant genes were defined as the genes count more than 4 times in each group. All data were analyzed using SPSS 25.0 software (Chicago, IL, USA). Pearson’s chi-squared (χ2) test, Fisher’s exact test, were used to test the associations between different variables. The Cox proportional hazard models was used to evaluate the relationship between KMT2C mutation and Disease free survival (DFS) in the patients cohorts. The results with p &amp;lt; 0.05 were considered statistically significant. 3. Results and Conclusions All 115 patients (primary ER status is positive) were divided into two groups, 70(60.87%) patients ER status remained positive while 45(39.14%) patients ER status transformed into negative. The histological type (p=0.008) and DFS (p=0.004) were significantly different in two subgroups. There were no significant correlations between the age at the time of diagnosis, BMI classification, menopausal status, surgery, histological grade, tumor size, lymph node status, metastasis, Ki67, adjuvant radiotherapy, neoadjuvant, metastasis site before second biopsy, first treatment after recurrent and first PFS after rebiopsy. Univariable analysis of DFS proved metastasis to be distinct risk factor for poor survival (hazard ratio [HR] &amp;gt; 1, p = 0.001). By contrast, neoadjuvant proved to be protective factor for better survival (hazard ratio [HR] &amp;lt; 1, p &amp;lt; 0.001). The surgery, histological type, histological grade, tumorsize, metastasis, neoadjuvant, first treatment after recurrent, first PFS after rebiopsy were subsequently analyzed with the multivariable Cox analysis. Metastasis (HR&amp;gt;1, p=0.007) and neoadjuvant (HR&amp;lt;1, p&amp;lt;0.001) remained independent prognostic factors of DFS. We compared the differentially mutated genes in the ER differential expression BC patient groups. Mutations in TP53 (n=24) and PIK3CA (n=19) occurred most frequently in both groups and account for 57.14% and 49.23% separately. Notably, mutations in KMT2C (n=6) was detected in ER+ to – subgroup and accounted for 37.5%. According to the results of NGS, the distribution of KMT2C mutations was different among the two cohorts. We identified the mutation in codon 321 was the hot spot of KMT2C in our patient cohort. Next, we used the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to analyze the enriched pathways of KMT2C. KEGG pathway analysis revealed that patients with KMT2C mutations harbored significantly more mutations in genes involved in the Ubiquitin mediated proteolysis and Lysine degradation signaling pathway. Table 1. Patients’ basic clinicopathological characteristics among two groups Table 2. Univariate and Multivariate Analysis Between Clinicopathological Characteristics and DFS of 115 BC patients Table 3. Mutated Genes Rank and patients number Citation Format: Xi Wang, Yongmei Yin, Ziyi Fu. Clinical profiling and comprehensive analysis of candidate genes related to breast cancer estrogen receptor intratumour heterogeneity [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-03-20.

Tumor necrosis factor-related lncRNAs predict prognosis and immunotherapy response for patients with lung adenocarcinoma.

Lung adenocarcinoma (LUAD) has become one of the most lethal cancers, for which the recurrence and survival rates remain unfavorable. The tumor necrosis factor (TNF) family is involved in tumorigenesis and tumor progression. Various long non-coding RNAs (lncRNAs) play important roles by mediating the TNF family in cancer. Therefore, this study aimed to construct a TNF-related lncRNA signature to predict prognosis and immunotherapy response in LUAD. The expression of TNF family members and their related lncRNAs in a total of 500 enrolled LUAD patients was collected from The Cancer Genome Atlas (TCGA). Univariate Cox and the least absolute shrinkage and selection operator (LASSO)-Cox analysis was used to construct a TNF family-related lncRNA prognostic signature. Kaplan-Meier (KM) survival analysis was used to evaluate survival status. The time-dependent area under the receiver operating characteristic (ROC) curve (AUC) values were used to assess the predictive value of the signature to 1-, 2-, and 3-year overall survival (OS). Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied to identify the signature-related biological pathways. Furthermore, tumor immune dysfunction and exclusion (TIDE) analysis was employed to evaluate immunotherapy response. A total of 8 TNF-related lncRNAs significantly associated with OS of LUAD patients were used to construct a TNF family-related lncRNA prognostic signature. According to risk score, these patients were divided into high- and low-risk subgroups. The KM survival analysis indicated that patients in the high-risk group showed significantly less favorable OS than that of low-risk group. The AUC values in predicting 1-, 2-, and 3-year OS were 0.740, 0.738, and 0.758, respectively. Moreover, the GO and KEGG pathway analyses demonstrated that these lncRNAs were closely involved in immune-related signaling pathways. The further TIDE analysis indicated that high-risk patients had a lower TIDE score than that of low-risk patients, indicating that high-risk patients may be appropriate candidates for immunotherapy. For the first time, this study constructed and validated a prognostic predictive signature of LUAD patients based on TNF-related lncRNAs, and the signature showed good performance to predict immunotherapy response. Therefore, this signature may provide new strategies for individualized treatment of LUAD patients.

Differential expression profile of microRNAs in the lung tissues of coal workers with pneumoconiosis and patients with silicosis.

The purpose of this study was to characterize the microRNA (miRNA) profile of the lung tissues from coal workers' pneumoconiosis (CWP) and silicosis and to analyze the changes in downstream genes, biological processes, and signaling pathways based on the differently expressed miRNAs. Lung tissues from three CWP patients, eight silicosis patients, and four healthy controls were collected and analyzed for their miRNA profiles using Affymetrix® GeneChip® miRNA Arrays. Differentially expressed miRNAs (DEMs) were identified between the different groups. The miRanda and TargetScan databases were used to predict the putative target genes, and volcano and heat maps were drawn. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were then performed to screen the DEMs-associated biological process and signaling pathways, respectively. Further identification with a comprehensive literature research involving particle exposure, fibrosis, inflammation and lung cancer were used to further screen DEMs of CWP and silicosis. Microarray data showed that 375 and 88 miRNAs were differentially expressed in CWP and silicosis lung tissues compared with healthy lung tissues, while 34 miRNAs were differentially expressed in CWP compared with silicosis lung tissues. The GO and KEGG pathway analyses showed that, the target genes were mainly enriched in the TGF-β, MAPK, p53 and other signal pathways. These results provided insight into the miRNA-related underlying mechanisms of CWP and silicosis, and they provided new clues for miRNAs as biomarkers for the diagnosis and differential diagnosis of these two diseases.

Mechanism of Xiezhuo Huayu Yiqi Tongluo Formula in the Treatment of Uric Acid Nephropathy Based on Network Pharmacology, Molecular Docking, and In Vivo Experiments.

Xiezhuo Huayu Yiqi Tongluo Formula (XHYTF) consists of 14 Chinese herbal medicines. In this study, we investigated the potential mechanism of XHYTF in the treatment of uric acid nephropathy (UAN) through network pharmacology, molecular docking, and in vivo methods. Using various pharmacological databases and analysis platforms, information on the active ingredients and targets of Chinese herbal medicine was collected, and UAN disease targets were retrieved using OMIM, Gene Cards, and NCBI. Then common target proteins were integrated. A Drug-Component-Target (D-C-T) map was constructed to screen core compounds and build a protein-protein interaction (PPI) network. Further, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed for common targets, and a Drug-Component-Target-Pathway (D-C-T-P) network diagram was constructed. The molecular docking simulation was performed to verify the binding affinity between core components and hub targets. Subsequently, the UAN rat model was established, followed by the collection of serum and renal tissues. The expression levels of indicators in the serum were determined using an enzyme-linked immunosorbent assay. The pathological changes of renal tissues were detected using H & E staining and Masson staining. The expression of related proteins in renal tissue was detected by western blot. In the study, 216 active ingredients and 439 targets in XHYTF were screened, and 868 targets were identified as being related to UAN. Among them, 115 were common targets. Based on the D-C-T network, quercetin, luteolin, β-sitosterol, and stigmasterol were observed to be the key active ingredients of XHYTF that were effective against UAN. The analysis of the PPI network revealed TNF, IL6, AKT1, PPARG, and IL1β as the 5 key targets. GO enrichment analysis revealed that the pathways were mainly concentrated in cell killing, regulation of signaling receptor activity, and other activities. Subsequently, KEGG pathway analysis revealed that multiple signaling pathways, including the HIF-1, PI3K-Akt, IL-17, and other signaling pathways, were closely related to the action of XHYTF. All 5 key targets were confirmed to interact with all core active ingredients. In vivo experiments indicated that XHYTF significantly reduced blood uric acid and creatinine levels, alleviated inflammatory cell infiltration in kidney tissues, reduced the levels of serum inflammatory factors such as TNF-α and IL1β, and ameliorated renal fibrosis in rats with UAN. Finally, western blot revealed decreased levels of PI3K and AKT1 proteins in the kidney, which confirmed the hypothesis. Collectively, our observations demonstrated that XHYTF significantly protects kidney function, including alleviation of inflammation and renal fibrosis via multiple pathways. This study provided novel insights into the treatment of UAN using traditional Chinese medicines.

Potential correlation of oral flora with pemphigus vulgaris – A case control study

Background/purposeOral flora is related to various immune-related diseases. Herein we explored the characteristics of oral flora in patients with pemphigus vulgaris (PV) and analyzed the correlation between oral flora and PV. Materials and methodsTwenty-two untreated patients with PV and 12 healthy controls (HC) were included in this case-control study. The characteristics of salivary microbiome were assessed by high-throughput sequencing using the 16S rRNA Illumina MiSeq approach, and differences between the PV and HC groups were determined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was applied to screen key metabolic pathways and preliminarily explore potential mechanisms underlying PV occurrence and development. ResultsThe abundance of oral flora in the PV group was significantly lower than that in the HC group, and there were characteristic changes. The relative abundance of Prevotella and Agrobacterium in the PV group was significantly higher than that in the HC group (P < 0.05) and that of Neisseria, Lautropia, and Fusobacterium was significantly lower (P < 0.05). There was a linear correlation between Prevotella and serum Dsg3 level in PV. KEGG pathway analyses indicated significant differences in nine metabolic pathways between the PV and HC groups (P < 0.05), namely carbohydrate metabolism, digestive system, neurodegenerative disease, glycan biosynthesis and metabolism, drug resistance: antimicrobial, infectious disease: viral, circulatory system, excretory system, and nervous system. ConclusionThe oral flora of patients with PV presented characteristic changes, and several metabolic pathways were affected, including N-glycan biosynthesis and metabolism. Prevotella spp. appear to require the most attention in PV. We believe that oral flora dysbacteriosis contributes to PV occurrence and development.

Five-hub genes identify potential mechanisms for the progression of asthma to lung cancer.

Previous studies have shown that asthma is a risk factor for lung cancer, while the mechanisms involved remain unclear. We attempted to further explore the association between asthma and non-small cell lung cancer (NSCLC) via bioinformatics analysis. We obtained GSE143303 and GSE18842 from the GEO database. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) groups were downloaded from the TCGA database. Based on the results of differentially expressed genes (DEGs) between asthma and NSCLC, we determined common DEGs by constructing a Venn diagram. Enrichment analysis was used to explore the common pathways of asthma and NSCLC. A protein-protein interaction (PPI) network was constructed to screen hub genes. KM survival analysis was performed to screen prognostic genes in the LUAD and LUSC groups. A Cox model was constructed based on hub genes and validated internally and externally. Tumor Immune Estimation Resource (TIMER) was used to evaluate the association of prognostic gene models with the tumor microenvironment (TME) and immune cell infiltration. Nomogram model was constructed by combining prognostic genes and clinical features. 114 common DEGs were obtained based on asthma and NSCLC data, and enrichment analysis showed that significant enrichment pathways mainly focused on inflammatory pathways. Screening of 5 hub genes as a key prognostic gene model for asthma progression to LUAD, and internal and external validation led to consistent conclusions. In addition, the risk score of the 5 hub genes could be used as a tool to assess the TME and immune cell infiltration. The nomogram model constructed by combining the 5 hub genes with clinical features was accurate for LUAD. Five-hub genes enrich our understanding of the potential mechanisms by which asthma contributes to the increased risk of lung cancer.

Identification of potential biomarkers for colorectal cancer by clinical database analysis and Kaplan-Meier curves analysis.

This study aimed to explore critical genes as potential biomarkers for the diagnosis and prognosis of colorectal cancer (CRC) for clinical utility. To identify and screen candidate genes involved in CRC carcinogenesis and disease progression, we downloaded microarray datasets GSE89076, GSE73360, and GSE32323 from the GEO database identified differentially expressed genes (DEGs), and performed a functional enrichment analysis. A protein-protein interaction network was constructed, and correlated module analysis was performed using STRING and Cytoscape. The Kaplan-Meier survival curve shows the survival of the hub genes. The expression of cyclin-dependent kinase (CDK1), cyclin B1 (CCNB1), and PCNA in tissues and changes in tumor grade were analyzed. A total of 329 DEGs were identified, including 264 upregulated and 65 downregulated genes. The functions and pathways of DEGs include the mitotic cell cycle, poly(A) RNA binding replication, ATP binding, DNA replication, ribosome biogenesis in eukaryotes, and RNA transport. Forty-seven Hub genes were identified, and biological process analysis showed that these genes were mainly enriched in cell cycle and DNA replication. Patients with mutations in CDK1, PCNA, and CCNB1 had poorer survival rates. CDK1, PCNA, and CCNB1 were significantly overexpressed in the tumor tissues. The expression of CDK1 and CCNB1 gradually decreased with increasing tumor grade. CDK1, CCNB1, and PCNA can be used as potential markers for the diagnosis and prognosis of CRC. These genes are overexpressed in colon cancer tissues and are associated with low survival rates in CRC patients.

RNA-Seq-based transcriptomics analysis during the photodynamic therapy of primary cells in secondary hyperparathyroidism.

The aim of this study was to identify changes in gene expression before and after 5-aminolevulinic acid-mediated photodynamic therapy (5-ALA-PDT) and to investigate the potential mechanism of 5-ALA-PDT based on ribonucleic acid sequencing (RNA-Seq) analysis. Secondary hyperparathyroidism (SHPT) primary cells were isolated from surgically excised specimens and exposed to laser light. The transcription profiles of SHPT primary cells were identified through RNA-Seq. Differentially expressed genes (DEGs) were identified. Enrichment of functions and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Quantitative real-time polymerase chain reaction (RT-qPCR) and western blot analysis were used to validate genes based on RNA-Seq results. In total, 1320 DEGs were identified, of which 1019 genes were upregulated and 301 genes were downregulated. GO and KEGG pathway analyses identified significantly enriched pathways in DEGs, including TGF beta in extracellular matrix (ECM), negative regulation of triglyceride biosynthetic process, protein heterodimerization activity, systemic lupus erythematosus, ECM-receptor interaction, focal adhesion and protein digestion and absorption. Protein-protein interaction (PPI) network analyses identified potential heat shock protein (HSP) interactions among the DEGs. Eight HSP genes were also identified that were most likely involved in 5-ALA-PDT, which were further validated by RT-qPCR and western blotting. The findings of this descriptive study reveal changes in the transcriptome profile during 5-ALA-PDT, suggesting that gene expression and mutation, signaling pathways, and the molecular network are altered in SHPT primary cells. The above findings provide new insight for further studies on the mechanisms underlying 5-ALA-PDT in SHPT.